Contacts of the helix formed by residues 187 - 199 (chain 2) in PDB entry 5IY8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 187 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1382 PRO* 5.7 2.9 - - - -
1832 GLY 3.5 8.7 - - - -
1842 LEU* 2.6 29.9 + - - +
1852 MET 3.4 4.2 + - - +
1862 LYS* 1.3 75.8 - - - +
1882 THR* 1.3 65.2 + - - +
1892 GLU* 4.2 8.7 + - - +
1902 PRO* 2.9 30.5 - - - +
1912 GLY* 3.8 5.4 + - - -
2322 GLU* 5.8 0.3 - - - +
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Residues in contact with THR 188 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382 PRO* 4.0 26.7 - - + -
1392 ASP 5.8 0.2 - - - +
1412 HIS* 5.1 5.3 - - + -
1872 SER* 1.3 70.0 - - - +
1892 GLU* 1.3 72.3 + - - +
1912 GLY* 2.8 14.0 + - - +
1922 GLU* 2.9 27.9 + - - +
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Residues in contact with GLU 189 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342 SER* 3.9 13.7 + - - -
1372 GLY* 4.7 2.9 - - - -
1382 PRO* 3.0 43.9 - - + +
1662 SER* 4.0 13.3 + - - +
1672 PRO* 5.6 0.9 - - - +
1702 ALA* 3.8 23.4 - - - +
1842 LEU* 5.3 6.2 - - - +
1872 SER* 4.6 5.1 + - - +
1882 THR* 1.3 81.6 - - - +
1902 PRO* 1.3 74.4 - - + +
1922 GLU* 2.7 36.6 - - + +
1932 PRO* 2.8 14.8 - - + +
2132 TRP* 5.2 7.6 - - + -
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Residues in contact with PRO 190 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842 LEU* 3.2 27.1 - - + +
1852 MET* 5.0 1.1 - - - +
1872 SER* 2.9 26.2 - - - +
1892 GLU* 1.3 92.6 - - + +
1912 GLY* 1.3 58.3 + - - +
1932 PRO* 4.6 3.8 - - + -
1942 PRO* 2.8 33.1 - - + +
2132 TRP* 4.7 19.3 - - + +
2172 LEU* 5.0 13.2 - - + -
2322 GLU* 4.2 25.8 - - + +
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Residues in contact with GLY 191 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1872 SER 3.8 4.0 + - - -
1882 THR* 2.8 10.2 + - - -
1902 PRO* 1.3 78.4 - - - +
1922 GLU* 1.3 62.5 + - - +
1942 PRO* 3.4 5.0 - - - +
1952 CYS* 2.9 22.4 + - - +
2322 GLU* 4.8 9.9 + - - -
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Residues in contact with GLU 192 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412 HIS* 2.7 67.2 + - + +
1632 MET* 5.4 1.3 - - - +
1662 SER* 4.5 8.3 + - - -
1672 PRO* 4.6 8.0 - - - +
1882 THR* 2.9 20.6 + - - +
1892 GLU* 2.7 44.9 - - - +
1912 GLY* 1.3 75.9 - - - +
1932 PRO* 1.3 75.8 - - + +
1952 CYS* 2.9 32.9 + - - -
1962 ILE* 3.1 6.7 + - + +
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Residues in contact with PRO 193 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632 MET* 6.4 1.1 - - + -
1672 PRO* 4.3 17.5 - - + -
1892 GLU* 2.8 24.4 - - + +
1902 PRO 4.4 0.2 - - - +
1912 GLY 3.5 0.4 - - - -
1922 GLU* 1.3 94.0 - - + +
1942 PRO* 1.3 72.9 - - + +
1962 ILE* 3.0 19.3 - - + +
1972 THR* 2.6 19.6 + - - +
2102 ALA* 4.5 13.7 - - + +
2132 TRP* 3.3 36.8 - - + +
2142 TYR* 5.9 1.1 - - + -
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Residues in contact with PRO 194 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1902 PRO* 2.8 26.0 - - + +
1912 GLY* 3.4 4.4 - - - +
1932 PRO* 1.3 91.3 - - + +
1952 CYS* 1.4 57.6 + - - +
1972 THR* 3.4 10.0 - - - +
1982 SER* 2.8 29.5 + - - -
2132 TRP* 5.5 1.1 - - + +
2142 TYR* 5.5 12.8 - - + -
2322 GLU* 6.4 0.2 - - + -
2352 SER* 3.3 41.1 - - - +
2382 PHE* 5.2 5.3 - - + -
2392 GLN* 5.3 9.0 - - + +
2612 PHE* 6.2 1.6 - - + -
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Residues in contact with CYS 195 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412 HIS* 5.6 3.4 - - - -
1912 GLY 2.9 12.8 + - - +
1922 GLU* 2.9 34.5 + - - +
1942 PRO* 1.4 77.5 - - - +
1962 ILE* 1.3 78.8 + - - +
1982 SER* 3.1 8.6 + - - -
1992 ALA* 3.1 22.0 + - - +
2022 GLN* 4.5 0.4 - - - -
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Residues in contact with ILE 196 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1412 HIS* 5.9 1.6 - - + -
1632 MET* 3.1 53.8 - - + -
1672 PRO* 5.5 2.2 - - + -
1922 GLU* 3.7 6.5 - - + +
1932 PRO* 3.0 18.6 - - + +
1952 CYS* 1.3 90.4 - - - +
1972 THR* 1.3 65.2 + - - +
1992 ALA 3.3 4.2 - - - +
2022 GLN* 2.9 52.0 + - + +
2062 LEU* 4.2 4.7 - - + +
2072 ASP* 4.5 4.6 - - - +
2102 ALA* 2.9 32.5 - - + +
2422 PHE* 5.6 0.3 - - - -
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Residues in contact with THR 197 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1932 PRO 2.6 22.4 + - - -
1942 PRO* 3.4 10.5 - - - +
1952 CYS 3.2 0.2 - - - -
1962 ILE* 1.3 81.0 - - - +
1982 SER* 1.3 57.6 + - - +
2072 ASP* 5.5 4.3 - - - +
2102 ALA* 4.1 6.3 - - - +
2112 GLN* 3.6 25.4 + - - +
2392 GLN* 3.1 47.4 + - + +
2422 PHE* 3.1 32.2 - - + +
2612 PHE* 4.5 3.3 - - - -
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Residues in contact with SER 198 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1942 PRO 2.8 13.6 + - - -
1952 CYS* 3.1 11.4 + - - -
1972 THR* 1.3 75.9 - - - +
1992 ALA* 1.3 61.5 + - - +
2002 GLY 3.4 1.2 + - - -
2382 PHE* 2.9 37.8 - - - -
2392 GLN* 5.9 1.3 - - - +
2412 SER* 5.1 1.9 + - - -
2422 PHE* 2.8 28.2 - - - +
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Residues in contact with ALA 199 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1952 CYS 3.1 8.2 + - - +
1962 ILE 3.3 4.1 + - - +
1982 SER* 1.3 78.8 - - - +
2002 GLY* 1.3 59.8 + - - +
2012 PHE* 2.9 30.5 - - + -
2022 GLN* 2.7 39.7 + - - +
2072 ASP* 5.4 0.2 - - - +
2422 PHE* 3.2 12.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il